A pen was a device used to write.
In the 19th and 20th centuries, fountain pens were used, a type of pen that had to be dipped in an inkwell full of ink every so often to sustain it. In 1963, these pens were believed to be "beneficial for [a student's] developing hand", and so a law was passed forcing school children to use them. Susan Foreman claimed that the inkwells at her school were stained blue from generations of use, and the Quink Ink-branded ink bottles that they carried would always pop and stain their bags. By the end of each day, she ended up with blue splotches in her fingernails, and, somehow, on her cheeks.
Despite this, the ballpoint pen had been invented by that year. Susan purchased one at W H Smith, and used it to write her diary. (PROSE: Time and Relative) Charley Pollard would only use a fountain pen at a hotel on 31 December 2007, as she came from the 1930s. (AUDIO: The Girl Who Never Was)
Ian Chesterton had a gold pen. As he passed it to the First Doctor, the pen disappeared right out of his hand. This was the work of the Animus, who had the capacity to control gold. (TV: The Web Planet)
By the 21st century, businesses regularly gave out pens. Representatives of Adipose Industries had to specify that they did not provide pens for their customers, without exception. (TV: Partners in Crime)
To insure that time flowed correctly, the Eleventh Doctor made sure that Amy Pond would use a red pen to message a past version of himself about 79B Aickman Road and Craig Owens' flat below it. (TV: The Lodger)
According to Susan Foreman, pens eventually became obsolete. The prominent form of writing dictating telepathically to machines that wrote it all out, checked for grammar and spelling and translated if necessary. (PROSE: Time and Relative) By the 52nd century, pens were no longer in general use, the nurses at the Sisters of the Infinite Schism having to order River Song one from an antique store so he could write in her diary. (GAME: The Eternity Clock)
John Harrison used a device disguised as a pen to maintain control of his slave Skullions. He electrified their collars when they disobeyed. Harrison's "pen" had 10 levels of punishment, level 10 completely killing them. The pen was destroyed by Lionel Carson who had been hypnotised by Serf. (TV: The Man Who Never Was)